That's odd because I didn't put it in separate folders and 2 incidents are running! One for my 996 and one for my 536, it's working normal??? I don't know if it's because of W10?
Each instance should be in different folders for two reasons.
Reason 1 is the options contained in the config(ProScan.cfg) file will not be shared. If restarting ProScan, the options are read from the ProScan.cfg file and will be the options from the last instance of ProScan unloaded. In other words; Let's say you stopped both instances of ProScan and the 536 instance was the last unloaded then when you restarted ProScan, both instances would be set for the 536 scanner type.
Reason 2 is the log files generated by ProScan. If you have the History, Recording, UID, or FTO logging then when you restart ProScan, the logs showing in the grids will be from the last instance unloaded.